Dear Javier,
As the manual says, {ibrav=0}: "crystal axis provided in input: see card
CELL_PARAMETERS".
With ibrav=0, you only specify the cell parameters. Remove space_group
and uniqueb, and specify all of the atoms in the cell.
Alternatively, if you use space_group, you specify only the
you saved my life, thanks a bunch Dr. Tamas
I'm only interested in dissociation reaction (SO2 to SO & O) , so i should only
consider image 1 & 2 only, based on AXSF file , for running NEB , right ? what
are these two steps you have seen ?
i'm doing micro-kinetic modeling for reaction
Dear Omer, dear all,
I would like to remind that there is absolutly no reason that the path
returned by the NEB is the real MEP.
The relaxed mep totaly depends on the initial guess of the MEP, which is most
of the time a linear interpolation between the initial and final states, except
if
As i see in the attached axsf file, the dissociation reaction occurs at image
2 , and there is no transition state between image 1 & 2 , does it mean it is
barrier-less reaction ?
On Monday, October 26, 2020, 06:31:22 PM GMT+4, Tamas Karpati
wrote:
please note that in case your
Dear Dr. Tamas your ideas are very helpful. Your are right.i have just noticed
that it is a surface reaction + diffusion of dissociated products (SO & O) to
most stable sites ( one reaction + 2 diffusion step). Dissociation occurs in
image 2 immediately , image 3,4,5 shows diffusion of SO
Dear Andrii
Thanks for the information.
Just this afternoon doing trial and error I get that the best way for
passing the unit cell parameters is using
ibrav and celdim according with manual, and for passing the asymmetric unit
for atoms and their respective equivalents then I have to use the
Dear Dr. Michal I have relaxed both initial and final structure with
forc_conv_thr = 1.0e-03 , and after convergence , each structure has a total
force that is less than 0.004.but after running NEB , it increased to the
above-mentioned values (0.02 & 0.03).However, i will try a tighter
yes, there is a barrier for the reverse reaction.i have check the initial &
final structure again , it was relaxed until force is less than 0.003.I do also
agree with you that i should use 1 neb with barrier, and this is what i'm
doing exactly.but for this dissociation reaction step (SO2 =
Dear Omer,
You have shown a figure of a MEP. Most probably image 4 is either R (reactant)
or P (product). In one case im2=R, im3=TS, im4=P (and im6 is the diffused P),
the other possibility is that im2=diffused R and im4=R then im6=P (im5=TS).
Try to judge which is which, then use R and P to
Dear Omer, dear prof. Kokalj and the QE developer team,
Thank you for the AXSF hint, the format and developing/sharing
XCrySDen and QE for so long!
Each is invaluable.
Best regards,
t
On Mon, Oct 26, 2020 at 6:13 PM Tone Kokalj wrote:
>
> On Mon, 2020-10-26 at 14:38 +, Omer Mutasim
On Mon, 2020-10-26 at 14:38 +, Omer Mutasim wrote:
> Dear Dr. Michal
> I have relaxed both initial and final structure with forc_conv_thr =
> 1.0e-03 ,
> but after running NEB , it increased to the above-mentioned values
> (0.02 & 0.03).
Which is OK, because the unit of force in pw.x is
Hello
I'm trying to use space-group directive in order to give only the atoms in
the asymmetric unit. But I don't know why I'm having problem with this.
My partial code is
...
!ibrav=0
space_group=14
uniqueb=.true.
nat=13
ntyp=6
ecutwfc=80.0
ecutrho=450.0
/
CELL_PARAMETERS
Dear Omer,
1, SO (being "locally" linear) is not really rotating (just nomenclature)
and such movements are unimportant in this case, I think
2, as for the NEB: as I said, choose the beginning and end images
of what you consider eg. step 1 and run a NEB like before,
except for
please note that in case your preoptimized first and/or last structures
are not the direct reactant and product structures but a R+diffusion
or P+diffusion step results, your MEP would (and it does) look
as if you have modelled a two (or even more) steps "reaction" even if
just one of them is
Dear Omer,
I'd like to underline what Antoine has said and suggest that
both your first and last structures are saddle points (of order K and L,
respectively), rather than minima. Also I agree that your reaction
is not barrierless -in accordance with chemical intuition.
To make it simple, I
Dear Omar,
This:
imageenergy (eV)error (eV/A)frozen
1 -92402.49729070.036606T
2 -92402.80086460.020347F
3 -92402.67892020.048720F
4 -92403.2726990
There is an energy barrier:
the one between your intermediate minima and your final state.
There is no barrier between initial and intermediate minima.
You should wonder why you have an intermediate minima that is lower in energy
(<0.4eV) than the final inserted molecule, this is why I was
Dear Dr. JayI have relaxed the initial and final structures before neb.
Regarding simulation box, i'm using sqrt(3)*sqrt(3) supercell, the other five
reaction steps converged well.However, i have seen in the literature that
similar catalyst resulted in such barrier-less dissociation.So my
Dear Hongyi Zhao,
> So, it would be better if we can further refine the result obtained by
> the second solution by some technical post-processing. This is just
> what I mean.
I would simply redo the vc-relaxation with tighter convergence thresholds for
the total energy and force, and then
Dear Omer,
I think your initial and final minima have not been well relaxed.
When you fix the initial and final structures in a neb you must have relaxed
them before, otherwise, you will have negative energy barriers.
Moreover, you may have rotation of molecules that return local minima if your
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